All T cell data

Sample Summary for all T cells

# A tibble: 7 x 2
                       Group     N
                      <fctr> <int>
1   Aged.Female.Brain.NoStim     5
2 Aged.Female.Brain.PlusStim     5
3     Aged.Male.Brain.NoStim     6
4   Aged.Male.Brain.PlusStim     4
5    Aged.Male.Spleen.NoStim     5
6  Aged.Male.Spleen.PlusStim     5
7    Young.Male.Brain.NoStim     5

Normalize and Filter the data

before normalization

                                 lib.size norm.factors
AgedFemale.Brain.NoStim.13_S10    9655634            1
AgedFemale.Brain.NoStim.14_S1    14866050            1
AgedFemale.Brain.NoStim.15_S6     6654543            1
AgedFemale.Brain.NoStim.16_S12   10970566            1
AgedFemale.Brain.NoStim.17_S8    12591901            1
AgedFemale.Brain.PlusStim.23_S11  4920738            1
AgedFemale.Brain.PlusStim.24_S9   6062158            1
AgedFemale.Brain.PlusStim.25_S5   9203922            1
AgedFemale.Brain.PlusStim.26_S1   3954801            1
AgedFemale.Brain.PlusStim.27_S8   2216762            1
AgedMale.Brain.NoStim.10_S9      19573103            1
AgedMale.Brain.NoStim.11_S10     18771250            1
AgedMale.Brain.NoStim.12_S11     20589456            1
AgedMale.Brain.NoStim.7_S6       24973886            1
AgedMale.Brain.NoStim.8_S7       10293283            1
AgedMale.Brain.NoStim.9_S8       16088402            1
AgedMale.Brain.PlusStim.19_S4     6391537            1
AgedMale.Brain.PlusStim.20_S3     2241662            1
AgedMale.Brain.PlusStim.21_S7     3850380            1
AgedMale.Brain.PlusStim.22_S2     1156594            1
AgedMaleSpleenNoStim30_S10        8998764            1
AgedMaleSpleenNoStim31_S7         9213356            1
AgedMaleSpleenNoStim32_S12        9650685            1
AgedMaleSpleenNoStim33_S3        14709415            1
AgedMaleSpleenNoStim34_S4        10176505            1
AgedMaleSpleenPlusStim36_S2      11101911            1
AgedMaleSpleenPlusStim37_S6       9932756            1
AgedMaleSpleenPlusStim38_S5       8586075            1
AgedMaleSpleenPlusStim39_S9       6745077            1
AgedMaleSpleenPlusStim40_S11     11188159            1
YoungMale.Brain.NoStim.2_S1      15470386            1
YoungMale.Brain.NoStim.3_S2      15558582            1
YoungMale.Brain.NoStim.4_S3      12213798            1
YoungMale.Brain.NoStim.5_S4      12781536            1
YoungMale.Brain.NoStim.6_S5      13326420            1

before filtering low-count genes

                               dim.y.counts.
total number of genes detected         38924
total sample number                       35

keep the genes that have more than 1 count per million (cpm) in at least 2 samples

                                      dim.y.counts.
total number of genes after filtering         12638
total sample number                              35

normalize the filtered genes across all samples

                                 lib.size norm.factors
AgedFemale.Brain.NoStim.13_S10    8450652        1.346
AgedFemale.Brain.NoStim.14_S1    12829959        1.249
AgedFemale.Brain.NoStim.15_S6     5775658        1.110
AgedFemale.Brain.NoStim.16_S12    9689366        1.200
AgedFemale.Brain.NoStim.17_S8    10768556        1.200
AgedFemale.Brain.PlusStim.23_S11  3558217        0.780
AgedFemale.Brain.PlusStim.24_S9   3879926        0.589
AgedFemale.Brain.PlusStim.25_S5   6195711        0.559
AgedFemale.Brain.PlusStim.26_S1   2247330        0.941
AgedFemale.Brain.PlusStim.27_S8   1083591        0.692
AgedMale.Brain.NoStim.10_S9      16743058        0.998
AgedMale.Brain.NoStim.11_S10     16260522        1.018
AgedMale.Brain.NoStim.12_S11     17521858        0.967
AgedMale.Brain.NoStim.7_S6       21581567        0.966
AgedMale.Brain.NoStim.8_S7        9004501        0.792
AgedMale.Brain.NoStim.9_S8       13854192        0.925
AgedMale.Brain.PlusStim.19_S4     4919751        0.797
AgedMale.Brain.PlusStim.20_S3     1531051        1.010
AgedMale.Brain.PlusStim.21_S7     2536233        0.631
AgedMale.Brain.PlusStim.22_S2      746962        0.859
AgedMaleSpleenNoStim30_S10        7317320        1.511
AgedMaleSpleenNoStim31_S7         7520542        1.461
AgedMaleSpleenNoStim32_S12        7904050        1.439
AgedMaleSpleenNoStim33_S3        12378836        1.460
AgedMaleSpleenNoStim34_S4         8315177        1.433
AgedMaleSpleenPlusStim36_S2       8927352        1.108
AgedMaleSpleenPlusStim37_S6       7522045        1.149
AgedMaleSpleenPlusStim38_S5       6625479        1.189
AgedMaleSpleenPlusStim39_S9       5092337        1.252
AgedMaleSpleenPlusStim40_S11      8254639        1.057
YoungMale.Brain.NoStim.2_S1      13277300        0.864
YoungMale.Brain.NoStim.3_S2      13244514        0.679
YoungMale.Brain.NoStim.4_S3      10078524        0.959
YoungMale.Brain.NoStim.5_S4      10953635        1.009
YoungMale.Brain.NoStim.6_S5      11336934        0.969

Overview on the data samples

MDS plot: to check the distance between each sample

MDS plot

MDS plot